RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data
Version 1.4.3

Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

AuthorHeiko Mannsperger with contributions of Stephan Gade
Date of publication2016-02-11 13:39:56
MaintainerAstrid Wachter <astrid.wachter@med.uni-goettingen.de>
LicenseLGPL
Version1.4.3
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RPPanalyzer", repos="http://R-Forge.R-project.org")

Popular man pages

dataII: Reverse phase protein array data, samples from a stimulation...
dataIII: Reverse phase protein array data from original cancer...
logList: Logarithmize (log2) the first two RPPA list elements, i.e....
plotTimeCourseII: Multiplot function for RPPA time course datasets
remove.arrays: Remove arrays from a RPPA data list
rppaList2ExpressionSet: Convert RPPA data into Expression Set
rppaList2Heatmap: Draw a heatmap with column side colors from a RPPA data
See all...

All man pages Function index File listing

Man pages

averageData: Average biological replicates over different slides.
calcLinear: Calculates sample concentrations using linear model fit
calcLogistic: Calculates sample concentrations using sigmoid model fit
calcSdc: Calculates the concentration of serial diluted samples
correctBG: Corrects for background in an RPPA data set
correctDilinterc: Dilution series intersect correction
curvePredictSigmoid: Sigmoidal curve prediction.
dataI: Reverse phase protein array rawdata, samples serially diluted
dataII: Reverse phase protein array data, samples from a stimulation...
dataIII: Reverse phase protein array data from original cancer...
dataPreproc: Data preprocessing
getErrorModel: Estimates error model parameters var0 (basal variance) and...
HKdata: Reverse phase protein array data of siRNA transfected cell...
logList: Logarithmize (log2) the first two RPPA list elements, i.e....
normalizeRPPA: Normalizes data in an RPPA data list
pick.high.conc: Select the highest concentration from serialy diluted samples
plotMeasurementsQC: Scatter Plots from an RPPA data
plotQC: Plot target and blank signal from RPPA control samples
plotqq: qq-plot and qq-line of an RPPA data set
plotTimeCourse: Draw time course from RPPA data
plotTimeCourseII: Multiplot function for RPPA time course datasets
read.Data: Read and Annotate RPPA rawdata
remove.arrays: Remove arrays from a RPPA data list
rppa2boxplot: Draws boxplots of groups of an RPPA data set including wilcox...
rppaList2ExpressionSet: Convert RPPA data into Expression Set
rppaList2Heatmap: Draw a heatmap with column side colors from a RPPA data
rppanalyzer-package: Read, annotate and normalize reverse phase protein array data...
S1.gpr: GenePix result files
sampledescription.old: sample description file
sampledescription.txt: sample description file
sample.median: Aggregate the replicates in an RPPA data set
select.measurements: Selects the measurement samples from an RPPA data list
select.sample.group: Selects samples from RPPA data
ser.dil.samples: Reverse phase protein array rawdata, samples serially diluted
simpleBoxplot: Draws boxplots of groups of an RPPA data set.
slidedescription.old: slide description file
slidedescription.txt: slide description file
test.correlation: Tests for correlations in RPPA data
write.Data: writes an RPPA data list into csv file

Functions

Files

DESCRIPTION
NAMESPACE
R
R/Sips.R
R/annotate.arrays.R
R/annotate.samples.R
R/array.id.R
R/averageData.R
R/calcLinear.R
R/calcLogistic.R
R/calcSdc.R
R/correctBG.R
R/correctDilinterc.R
R/create.ID.col.R
R/createColumnIndices.R
R/curveFitLinear.R
R/curveFitSigmoid.R
R/curvePredictLinear.R
R/curvePredictSigmoid.R
R/dataPreproc.R
R/dil.ser.id.R
R/g.link.R
R/get.Splines.R
R/getErrorModel.R
R/heatmapcolors.R
R/logList.R
R/median.raw.R
R/norm.BCA.R
R/norm.static.I.R
R/norm.static.II.R
R/norm.texas.R
R/normalizeRPPA.R
R/pick.high.conc.R
R/plotDilutionSeries.R
R/plotHeatmap.R
R/plotMeasurementsQC.R
R/plotQC.R
R/plotTimeCourse.R
R/plotTimeCourseII.R
R/plotqq.R
R/protein.con.R
R/read.Data.R
R/read.gpr.R
R/read.sampledescription.R
R/read.slidedescription.R
R/remove.arrays.R
R/rppa2boxplot.R
R/rppaList2ExpressionSet.R
R/rppaList2Heatmap.R
R/sample.median.R
R/samples.id.R
R/select.measurements.R
R/select.sample.group.R
R/simpleBoxplot.R
R/slides.id.R
R/spotbyspot.R
R/sub.ID.R
R/test.correlation.R
R/write.Data.R
build
build/vignette.rds
data
data/HKdata.RData
data/dataI.RData
data/dataII.RData
data/dataIII.RData
data/sampledescription.old.txt.gz
data/ser.dil.samples.RData
data/slidedescription.old.txt.gz
inst
inst/doc
inst/doc/RPPanalyzer.R
inst/doc/RPPanalyzer.pdf
inst/doc/RPPanalyzer.rnw
inst/extdata
inst/extdata/FCF_Slide.gpr
inst/extdata/S1.gpr
inst/extdata/S2.gpr
inst/extdata/S4.gpr
inst/extdata/Slide1.gpr
inst/extdata/Slide2.gpr
inst/extdata/Slide3.gpr
inst/extdata/sampledescription.txt
inst/extdata/slidedescription.txt
man
man/HKdata.Rd
man/S1.gpr.Rd
man/averageData.Rd
man/calcLinear.Rd
man/calcLogistic.Rd
man/calcSdc.Rd
man/correctBG.Rd
man/correctDilinterc.Rd
man/curvePredictSigmoid.Rd
man/dataI.Rd
man/dataII.Rd
man/dataIII.Rd
man/dataPreproc.Rd
man/getErrorModel.Rd
man/logList.Rd
man/normalizeRPPA.Rd
man/pick.high.conc.Rd
man/plotMeasurementsQC.Rd
man/plotQC.Rd
man/plotTimeCourse.Rd
man/plotTimeCourseII.Rd
man/plotqq.Rd
man/read.Data.Rd
man/remove.arrays.Rd
man/rppa2boxplot.Rd
man/rppaList2ExpressionSet.Rd
man/rppaList2Heatmap.Rd
man/rppanalyzer-package.Rd
man/sample.median.Rd
man/sampledescription.old.Rd
man/sampledescription.txt.Rd
man/select.measurements.Rd
man/select.sample.group.Rd
man/ser.dil.samples.Rd
man/simpleBoxplot.Rd
man/slidedescription.old.Rd
man/slidedescription.txt.Rd
man/test.correlation.Rd
man/write.Data.Rd
vignettes
vignettes/Figure1.png
vignettes/RPPanalyzer.rnw
vignettes/b2-clj4700dn-p2
vignettes/papers_RPPanalyzer.bib
vignettes/workflow_RPPanalyzer.png
RPPanalyzer documentation built on May 21, 2017, 12:38 a.m.

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